The alarm blares at 5:45 a.m., but I needn’t have bothered to set it. Within minutes, heavy footsteps sound on the wooden staircase, clomping upstairs. It is the sound of oyster farmers on their way to grab boxes, boots, buoys and assorted metal tools. Today, I am one, too.

When I met Patrick Hudson at his True Chesapeake Oyster farm at St. Jerome Creek in Southern Maryland a couple of months ago, we began talking about how no two days are alike on an oyster farm. Oyster farmers are riggers — learning from past mistakes, making it up as they go along, hoping that weather and tides work in their favor. With more than a dozen farms operating in Maryland, and many more in neighboring Virginia, Hudson can turn to fellow farmers like Chesapeake Gold’s Johnny Shockley for advice — and he does.

A new coalition of farmers, scientists, poultry companies and government agencies is working on the Delmarva Peninsula to determine the best ways to both manage nutrient pollution in the Chesapeake Bay and keep farmers in business.

The initiative, called the Delmarva Land and Litter Challenge, released its first report in August. In it, the group states that the farms have not made as much progress in cleanup as they or the regulators would like because technology that could reduce pollution is slow to develop and data on how best to employ it is not as accurate as it needs to be.

The group is focusing on two themes: better technologies to transform manure into energy and assistance in incorporating land-applied manure into the soil so that it’s less likely to run off and is more available to crops.

Like many farmers, John Swaine worked hard to control the runoff coming from the 1,800 acres of row crops he farms in Talbot County. He put in cover crops to absorb the excess nitrogen in the soil. He stopped tilling much of the Maryland farm’s soil to stem erosion, and he used integrated pest management to minimize his spraying of pesticides.

Still, after a rainstorm — a prolonged one or just one of the 20-minute gushers common during summers on the Eastern Shore — the water in his drainage ditch ran turbid. Swaine thought maybe he could do something more.

“I live right here,” he said, pointing to a farmhouse two miles from the Oxford-Bellevue Ferry in Royal Oak. “It bothered me. It still bothers me. But some of it is beyond what we’re capable of controlling.”

Rod Walker stretched his arm out toward the mountains north of his 1,500 acres abutting Shenandoah National Park in Albemarle County. The view was possible because of an opening where dead trees, strangled by oriental bittersweet and grapevine, had been removed.

Bittersweet, ailanthus, Japanese stilt grass, garlic mustard — these are some of the invasive species that Walker has targeted in a control plan he’s implementing a step at a time.

It’s no easy task, because invasive species — defined as a nonnative species that when introduced causes economic or environmental harm or harm to human health — often outcompete natives, thus interfering with ecological succession and, in turn, promoting other invasive plants and animals. Invasives significantly affect the food web; alter soil chemistry and nutrient cycling; change hydrology; and increase the severity of fires.

The cownose ray is majestic, a hawk of the sea. Approaching a school of the kite-shaped creatures through clear waters is a thrill for divers and boaters every spring, when the rays return to the Chesapeake’s shallows. They glide along, wings slicing through the waters, with a grace that belies their heavy bodies.

But watermen say the cownose rays chomp on the oysters, soft clams, razor clams and menhaden that make up some of the last fisheries. Oyster farmers complain they devour the spat-on-shell crops and force farms to invest in expensive cage gear. They can destroy grass beds that shelter crabs. They can also injure fishermen with the spikes at the base of their tails.

Far fewer would summon to mind Saxis, VA, population “200 on a busy July weekend, 100 on a cold January day,” according to Moody “M. K.” Miles III, the town’s historian, and “local” enough that his family’s name adorns now- collectible oyster cans.

Wearing more protective gear than he needs for gardening, Bill Brower stepped inside a knee-high fence to pluck a few ripe tomatoes from an overgrown vine.

“I encourage people to take a bite,” he said, wearing the hardhat and neon vest that’s required at DC Water’s Blue Plains Advanced Wastewater Treatment Plant.

The cherry tomato tastes as good as it should in late July. Brower explains that it was grown with the help of composted biosolids — organic matter that has been recycled from the sewage of the District of Columbia’s residents.

In a little more than two years, states in the Bay watershed will need to provide evidence that the nutrient and sediment pollution reduction actions they report are resulting in improvements in the real world — not just on paper.

The six states in the Bay watershed, and the District of Columbia, submitted draft plans this summer showing how they would accomplish that.

But an independent panel of outside experts that reviewed the drafts found a lot of work remained to be done.

Another Maryland county has made it illegal to use coal tar pavement products that are known to contribute pollutants to area streams and the Chesapeake Bay, becoming the third municipality in the region to do so.

Prince George’s County joined the District of Columbia and Montgomery County, MD, when its ban of coal tar pavements went into effect at the beginning of July. This category of thick brown or black liquid is a byproduct of the carbonization of coal that has been used for decades to seal driveways, parking lots, playgrounds and recreational trails to extend the life of asphalt and concrete surfaces.

Sorting through a pile of scraggly tree roots in early June, Brian Mayell conducted a quick autopsy.

“On none of these, to me, does it look like the root system was the culprit,” he said.

That’s good news for the general manager of Casey Tree Farm, who, among other duties, is charged with growing better trees for the nonprofit charged with restoring, enhancing and protecting the tree canopy of the nation’s capital, a goal it has been working toward for nearly 15 years.

Is it safe to swim in the Chesapeake Bay and its tributaries? Depends on who you are, and whom you ask.

Under the 2000 Beach Act, the EPA required states to establish water quality criteria for beaches. States and counties are supposed to test the beaches regularly and post warnings when the beaches exceed their allowable levels for bacteria. In Maryland, health officials advise swimmers to stay out of the water within 72 hours of a rainstorm.

Leakin Park, on Baltimore’s western fringe, is one of the largest urban woodland parks on the East Coast. It includes a 15-mile biking trail, a nature center, several restored historic structures and sweeping views of the Gywnns Falls. There is a mansion, art walk, old waterwheel and plenty of places to have a picnic or climb on the monkey bars.

But many residents of Baltimore know Leakin Park for something else — the bodies. From the 1940s until just a few years ago, dozens of corpses were dumped there. Headlines in the Baltimore Sun announced the bodies discovered in the park, many found in stages of gruesome decay as they were deep in a wilderness area where daylight visitors seldom roamed.

The Somerset County Planning Commission is considering tighter zoning regulations for poultry houses, but has rejected both a moratorium on building proposed new houses that are much larger than current poultry houses and a health ordinance that would have allowed prosecution for violations as some neighbors had requested.

The commission has been studying its zoning ordinance for the better part of a year, since residents along the Backbone Road corridor complained about the size of the poultry houses being built in Princess Anne and the way they are being integrated into a rural, residential neighborhood. Within three miles of Backbone Road, 50 large chicken houses have already been built, and more than 67 are in various stages of permitting and construction throughout the county. Many of these chicken houses are large buildings on lots as small as 10 acres, each designed to accommodate 20,000 birds per six-week cycle.

Most of the children who attend Lakeland Elementary School don’t have apple trees in their backyards. They live in city row houses in West Baltimore, and they see a lot of asphalt, strip malls and chain-link fences.

Recently, the view at their school changed. Lakeland is one of three Baltimore schools that have gotten an orchard — dozens of apple and pear trees that will soon bear fruit. The trees came courtesy of the Baltimore Orchard Project, an organization founded three years ago to glean and distribute fruit already growing and going to waste and to plant fruit trees in vacant and used city spaces.

The 3rd U.S. Circuit Court of Appeal Monday upheld the EPA’s authority to require an expansive Chesapeake Bay cleanup plan, firmly rebuffing challenges by farm groups and a coalition of states.

The court in its 60-page ruling stated that the EPA’s Chesapeake Bay Total Maximum Daily Load, or TMDL, “is reasonable and reflects a legitimate policy choice,” while calling various arguments by the American Farm Bureau Federation and its allies “illogical,” “unpersuasive,” “defies common sense” and, in one instance, “long on swagger but short on specificity.”